.intValue();
}
}
- alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
- // was
- // duplicated
- // earlier
+ // annotation was duplicated earlier
+ alignment.addAnnotation(sequences[i].getAnnotation()[a]);
+ // take care of contact matrix too
+ ContactMatrixI cm=sequences[i].getContactMatrixFor(sequences[i].getAnnotation()[a]);
+ if (cm!=null)
+ {
+ alignment.addContactListFor(sequences[i].getAnnotation()[a], cm);
+ }
+
alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
a);
}